BP 204
Focus Paper: Ligand Binding - Stroud:
P1) Fersht AR; Shi JP; Knill-Jones J; Lowe DM; Wilkinson AJ; Blow DM; et al. Hydrogen
bonding and biological specificity analysed by protein engineering. Nature, 1985 Mar
21-27, 314(6008):235-8.
• Energetic accounting for a hydrogen bond
• Paired-to-unpaired hydrogen bonds to charged moieties
• Balancing the equation of hydrogen bonds versus solvent
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P2) Livnah O; Stura EA; Johnson DL; Middleton SA; Mulcahy LS; Wrighton NC; Dower
WJ; Jolliffe LK; Wilson IA. Functional mimicry of a protein hormone by a peptide agonist:
the EPO receptor complex at 2.8 A Science, 1996 Jul 26, 273(5274):464-71.
• Biology of selection: ‘phage display’; why dimerizing ligands selected?
• Avidity. Additivity of free energy contributors
• Buried surface areas and affinity
• Transmembrane signaling by cytokine receptors depends on dimerization
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P3) Robert C. Rizzo, De-Ping Wang, Julian Tirado-Rives, and
William L. Jorgensen Validation of a Model for the Complex of HIV-1
Reverse Transcriptase with Sustiva through Computation of Resistance
Profiles
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P4) David E. Shaw,1,2* Paul Maragakis,1† Kresten Lindorff-Larsen,1† Stefano
Piana,1† Ron O. Dror,1 Michael P. Eastwood,1 Joseph A. Bank,1 John M.
Jumper,1 John K. Salmon,1 Yibing Shan,1 Willy Wriggers Atomic-Level
Characterization of the Structural Dynamics of Proteins
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P5) Chimera tutorial: http://bit.ly/LBQr04
(http://www.cgl.ucsf.edu/chimera/data/tutorials/bp204/classdata.html)
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P6) Zhou, Y; Morals-Cabral, JH; Kaufman, A., MacKinnon, R. Chemistry of ion
coordination and hydration revealed by a K+ channel-Fab complex at 2.0 Å resolution.
Nature, 2001 Nov 01, (414):43-48.
• Basis for coordinating K+ ions – the pathway
• Compensation for lipids in the center
• Selectivity for K+ versus other ions
• Hydrophobic exit port
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P7). Erlanson,DA; Braisted, AC; Raphael, DR; Randal, Mike; Stroud,RM;
Gordon, EM; Wells, JA. Site-directed ligand discovery. PNAS. 2000 Aug 15,
97(17)9367-9372.
• Facing problems for Drug Discovery
• Tethering – Why? How? Reducing potential
• Additivity of energy
Jencks WP. On the attribution and additivity of binding energies. Proc Natl
Acad Sci U S A. 1981;78(7):4046-50.
• The conundrum of non-additivity
• Fragmenting Biotin
• Entropy reduction
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P8) Rasmussen SG, DeVree BT, Zou Y, Kruse AC, Chung KY, Kobilka TS, et al.
Crystal structure of the beta2 adrenergic receptor-Gs protein complex. Nature.
2011;477(7366):549-55.
•
•
•
•
Heterotrimeric G-protein complex
Llama antibodies/nanobodies cubic lipidic phases
Crystallogenesis
Activation, interaction surface
Chun E, Thompson AA, Liu W, Roth CB, Griffith MT, Katritch V, et al. Fusion partner
toolchest for the stabilization and crystallization of G protein-coupled receptors.
Structure. 2012;20(6):967-76.
• Protein engineering for stability
• Size exclusion chromatography and flexibility
• Protein diffusion and crystallization
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Focus Papers: Enzymes and Catalysis: Miller/Gross
P9) TBD
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P10) Jiang L, Althoff EA, Clemente FR, Doyle L, Röthlisberger D, Zanghellini A,
Gallaher JL, Betker JL, Tanaka F, Barbas III CF, Hilvert D, Houk KN, Stoddard
BL, Baker D. De novo computational design of retro-aldol enzymes. Science.
2008;319:1387-91.
• initial designs for catalysis – levels of success and kinetic behaviors
Lassila JK, Baker D, Herschlag D. Origins of catalysis by computationally
designed retroaldolase enzymes. PNAS. 2010;107:4937-42.
• Testing designed catalytic “features” for actual contribution
• model & enzyme rate-pH profile and Bronsted analysis of rate vs pKa
• teasing out source of unexpected kinetics and how to work around
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P11) Neal SE, Eccleston JF, Hall A, Webb MR. Kinetic Analysis of the hydrolysis
of GTP by p21N-ras. J. Biol. Chem. 1988;263:19718-22.
• Ras GTPase activity is extremely low – what is rate limiting?
• single turnover methods to measure association, dissociation, hydrolysis rate
constants
• pulse-chase methods to measure partitioning of intermediates
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P12) Scheffzek K, Ahmadian MR, Kabsch W, Wiesmüller L, Lautwein A, Schmitz
F, Wittinghofer A. The Ras-RasGAP complex structural basis for GTPase
activation and its loss in oncogenic Ras mutants. Science. 1997;277:333-38.
• protein-protein interaction provides key residue for TS activation
Gideon P, John J, Frech M, Lautwein A, Clark R, Scheffler JE, Wittinghofer A.
Mutational and kinetic analyses of the GTPase-activating protein (GAP)-p21
interaction: the C-terminal domain of GAP is not sufficient for full activity.
Mol.Cell.Biol. 1992;12:2050-56.
• novel method to measure kinetics of activation of hydrolysis
• role for additional protein-protein interaction domains
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P13) Milburn MV, Tong L, deVos AM, Brunger A, Yamaizumi Z, Nishimura S, et
al. Molecular switch for signal transduction: structural differences between
active and inactive forms of protooncogenic ras proteins. Science. 1990;247
Kraulis PJ, Domaille PJ, Campbell-Burk SL, Van Aken T, Laue ED. Solution
structure and dynamics of ras p21.GDP determined by heteronuclear three- and
four-dimensional NMR spectroscopy. Biochemistry. 1994
• GTPases are moleculer switches controlled by nucleotide state
• Conformational changes of “Switch” regions detected by crystallography provides
insights into interactions of RAS with effectors
• Mobility of individual residues can be measured by NMR and provides insights into
regulation of enzymes by interaction with ligands or other proteins
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P14) Worthylake DK, Rossman KL, Sondek J. Crystal structure of Rac1 in
complex with the guanine nucleotide exchange region of Tiam1. Nature. 2000;408
Aghazadeh B, Lowry WE, Huang XY, Rosen MK. Structural basis for relief of
autoinhibition of the Dbl homology domain of proto-oncogene Vav by tyrosine
phosphorylation. Cell. 2000;102(5):625-33.
• GEF proteins activate GTPases by promoting exchange of GDP for GTP
• The exchange reaction requires alleviation of GEF autoinhibition
• The mechanism of activation requires an order-to-disorder transition that can be
followed by NMR
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P15) Li P, Martins IR, Amarasinghe GK, Rosen MK. Internal dynamics control
activation and activity of the autoinhibited Vav DH domain. Nat Struct Mol Biol.
2008;15(6):613-8.
• Proteins conformational transitions in GEF can limit rates of activation
• Transitions from major to minor populated allow post-translational modification to
consolidate activated state
• NMR can be used to measure conformational excursions on pathway to activation
Focus Papers for Protein Folding: Agard
1) Eriksson AE; Baase WA; Zhang XJ; Heinz DW; Blaber M; Baldwin EP; Matthews BW.
Response of a protein structure to cavity-creating mutations and its relation to the
hydrophobic effect. Science 255:178-183. (1992)
• Quantitative measurement of contribution of hydrophobic effect to protein stability
• Deletions result in cavities within the protein that compact to differing degrees
• Energetics of cavity formation comparable to hydrophobic effect
• Rationalizes energetic consequences of side chain mutations-after contradictions
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2) Riddle DS, Santiago JV, Bray-Hall ST, Doshi N, Grantcharova VP, Yi Q, Baker D
Functional rapidly folding proteins from simplified amino acid sequences Nature Struct
Biol 4:805-809 (1997)
• How complex a sequence “alphabet” is required to code a stable protein fold?
• Is the folding rate of small protein domains optimized through evolution?
• Use of phage display for simplifying proteins
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3) Hughson,F.M., Wright, P.E., Baldwin, R.L. Structural characterization of a partly
folded apomyoglobin intermediate Science 249:1544-1548 (1990).
• Molten globules are thought to be critical intermediates along folding pathways
• Structure of a molten globule
• Use of hydrogen exchange to study properties of folding reactions
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4) Chamberlain AK; Handel TM; Marqusee S. Detection of rare partially folded
molecules in equilibrium with the native conformation of RNaseH Nature Structure
Biology 3:782-7 (1996).
• Rare conformational states are accessible from the native state
• Correlation between relative stability and folding pathways
• Domains in a structure have different stabilities
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5) Netzer WJ, Hartl FU. Recombination of protein domains facilitated by co-translational
folding in eukaryotes Nature 388:343-349 (1997)
• Comparison; protein folding machinery in prokaryotes and eukaryotes
• Fundamental differences may be adapted for folding of different kinds of proteins
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Focus Papers: Protein-Protein Interactions: Fletterick
1) Schuster SC; Swanson RV; Alex LA; Bourret RB; Simon MI. Assembly and function of a
quaternary signal transduction complex monitored by surface plasmon resonance. 1993
Nature, 365(6444):343-7.
• Measuring association and dissociation of proteins
• Role of ATP driven phosphorylation and covalent modification in complex stability
• Role of ligand binding to receptor in promoting assembly
• SPR to derive binding constants
• Quaternary signal transduction complex controls chemotaxis
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2) Horton N; Lewis M. Calculation of the free energy of association for protein
complexes. (1992) Protein Science 1(1):169-81.
• Thermodynamics of Protein Assembly
• Structural Change on complexation
• Empirical fitting of Atomic Interactions with Free Energy of Association
• Estimate of free energy of H bonds and charge interactions in protein complexes and role
of hydrophobic effect
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3) Chothia C; Lesk AM; Tramontano A; Levitt M; Smith-Gill SJ; Air G; Sheriff S; Padlan EA;
Davies D; Tulip WR; et al. Conformations of immunoglobulin hypervariable regions.
Nature, 1989 Dec 21-28, 342(6252):877-83.
• Definition of IgG fold
• Definition of CDR’s and their conformations
• Target sites on antigens and Fab’s
• Structural changes, characterization of interfaces
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4) Clackson T; Ultsch MH; Wells JA; de Vos AM. Structural and functional analysis of
the 1:1 growth hormone:receptor complex reveals the molecular basis for receptor
affinity. Journal of Molecular Biology, 1998 Apr 17, 277(5):1111-28.
• Structure of Growth hormone with its receptor
• Mutagenesis and Affinity define important interfaces
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5) Russo AA; Jeffrey PD; Patten AK; Massague J; Pavletich NP. Crystal structure of the
p27Kip1 cyclin-dependent-kinase inhibitor bound to the cyclin A-Cdk2 complex.
Nature, 1996 Jul 25, 382(6589):325-31.
• Multiple interactions build a three-protein complex
• Protein mimic of ATP
• Changes in protein structure on complex formation
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Focus Papers: Nucleic acid-Protein Interactions: Frankel
1) Weeks, K. M. and Crothers, D. M. Major groove accessibility of RNA. 1993 Science 261,
1574-1577.
• The major groove provides a prime recognition surface in nucleic acids
• RNA and DNA structures are very different
• Discontinuities in RNA helices make virtually all base pairs available for recognition
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2) Murray, J. B., Terwey, D. P., Maloney, L., Karpeisky, A., Usman, N., Beigelman, L., and
Scott, W. G. The structural basis of hammerhead ribozyme self-cleavage. 1998 Cell 92,
665-673.
• RNAs adopt complex folds
• RNAs can perform chemical reactions
• Metal ions are important for structure and catalysis
• RNAs can undergo major conformational change
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3) Sclavi, B., Sullivan, M., Chance, M. R., Brenowitz, M., and Woodson, S. A. RNA folding
at millisecond intervals by synchrotron hydroxyl radical footprinting. 1998 Science 279,
1940-1943.
• RNA folding is ordered but does not necessarily follow a single pathway
• Secondary structures (helices) assemble into higher order structures
• Kinetic traps are possible
• Folding time scales are similar to proteins
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4) Rastinejad, F., Perlmann, T., Evans, R.M., and Sigler, P.B. Structural determinants of
nuclear receptor assembly on DNA direct repeats. 1995 Nature 375, 203-211.
• DNA-binding proteins often share common structural motifs
• The major groove, minor groove, and backbone provide specific recognition points
• Water molecules often are located at protein-nucleic acid interfaces
• Oligomeric arrangements can generate different specificities
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5) Price, S. R., Evans, P. E., and Nagai, K. Crystal structure of the spliceosomal U2B"-U2A'
protein complex bound to a fragment of U2 small nuclear RNA. 1998 Nature 394, 645650.
• RNA loops provide important recognition features
• Both RNA and protein often show induced fit upon binding
• Recognition surfaces can be remodeled to generate different specificities
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